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[Gmsh] gmshToFoam generates patches with 0 faces and 0 points |
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June 2, 2020, 02:32 |
gmshToFoam generates patches with 0 faces and 0 points
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#1 |
New Member
Join Date: Jan 2019
Posts: 10
Rep Power: 7 |
I have converted my gmsh generated mesh to OpenFOAM format using gmshToFoam, and everything is fine, and mesh is properly converted. checkMesh passes with flying colours. But, I end up with patches (i.e., my Physical surfaces in gmsh) that have 0 faces and 0 points on them! This obviously breaks simulation later on as I cannot assign velocity or pressure to these boundaries. Please help, any ideas is appreciated. I can change the code if need be. I can code in C++, just give me a pointer on what is going on.
Gmsh shows that there are faces on these surfaces, but they are not converted somehow. Here is the output of mesh conversion, plus checkMesh output at the end: Info : Running 'gmsh -format msh22 -o mesh/pipe2.msh -3 -smooth 3 mesh/pipe2.geo' [Gmsh 4.5.6, 1 node, max. 1 thread] Info : Started on Mon Jun 1 23:17:49 2020 Info : Reading 'mesh/pipe2.geo'... Info : Extrusion layer cycle detected for curve 2 Info : Extrusion layer cycle detected for curve 6 Info : Extrusion layer cycle detected for curve 15 Info : Extrusion layer cycle detected for curve 2 Info : Extrusion layer cycle detected for curve 6 Info : Extrusion layer cycle detected for curve 15 Info : Done reading 'mesh/pipe2.geo' Info : Meshing 1D... Info : [ 0 %] Meshing curve 1 (Line) Info : [ 10 %] Meshing curve 2 (Line) Info : [ 10 %] Meshing curve 3 (Line) Info : [ 10 %] Meshing curve 4 (Line) Info : [ 20 %] Meshing curve 5 (Line) Info : [ 20 %] Meshing curve 6 (Line) Info : [ 20 %] Meshing curve 7 (Line) Info : [ 20 %] Meshing curve 8 (Line) Info : [ 30 %] Meshing curve 9 (Line) Info : [ 30 %] Meshing curve 10 (Line) Info : [ 30 %] Meshing curve 11 (Line) Info : [ 30 %] Meshing curve 12 (Line) Info : [ 40 %] Meshing curve 13 (Line) Info : [ 40 %] Meshing curve 14 (Line) Info : [ 40 %] Meshing curve 15 (Line) Info : [ 50 %] Meshing curve 16 (Line) Info : [ 50 %] Meshing curve 17 (Extruded) Info : [ 50 %] Meshing curve 18 (Extruded) Info : [ 50 %] Meshing curve 19 (Extruded) Info : [ 60 %] Meshing curve 20 (Extruded) Info : [ 60 %] Meshing curve 21 (Extruded) Info : [ 60 %] Meshing curve 22 (Extruded) Info : [ 60 %] Meshing curve 23 (Extruded) Info : [ 70 %] Meshing curve 24 (Extruded) Info : [ 70 %] Meshing curve 25 (Extruded) Info : [ 70 %] Meshing curve 26 (Extruded) Info : [ 80 %] Meshing curve 27 (Extruded) Info : [ 80 %] Meshing curve 28 (Extruded) Info : [ 80 %] Meshing curve 29 (Extruded) Info : [ 80 %] Meshing curve 30 (Extruded) Info : [ 90 %] Meshing curve 31 (Extruded) Info : [ 90 %] Meshing curve 32 (Extruded) Info : [ 90 %] Meshing curve 33 (Extruded) Info : [ 90 %] Meshing curve 34 (Extruded) Info : [100 %] Meshing curve 35 (Extruded) Info : [100 %] Meshing curve 36 (Extruded) Info : [100 %] Meshing curve 37 (Extruded) Info : Done meshing 1D (0.030967 s) Info : Meshing 2D... Info : [ 0 %] Meshing surface 20 (Plane, Frontal-Delaunay) Info : [ 10 %] Meshing surface 21 (Plane, Frontal-Delaunay) Info : [ 10 %] Meshing surface 22 (Plane, Frontal-Delaunay) Info : [ 20 %] Meshing surface 23 (Plane, Frontal-Delaunay) Info : [ 20 %] Meshing surface 24 (Extruded) Info : [ 30 %] Meshing surface 25 (Extruded) Info : [ 30 %] Meshing surface 26 (Extruded) Info : [ 40 %] Meshing surface 27 (Extruded) Info : [ 40 %] Meshing surface 28 (Extruded) Info : [ 50 %] Meshing surface 29 (Extruded) Info : [ 50 %] Meshing surface 30 (Extruded) Info : [ 60 %] Meshing surface 31 (Extruded) Info : [ 60 %] Meshing surface 32 (Extruded) Info : [ 70 %] Meshing surface 33 (Extruded) Info : [ 70 %] Meshing surface 34 (Extruded) Info : [ 80 %] Meshing surface 35 (Extruded) Info : [ 80 %] Meshing surface 36 (Extruded) Info : [ 90 %] Meshing surface 37 (Extruded) Info : [ 90 %] Meshing surface 38 (Extruded) Info : [100 %] Meshing surface 39 (Extruded) Info : [100 %] Meshing surface 40 (Extruded) Info : Done meshing 2D (0.300156 s) Info : Meshing 3D... Info : Meshing volume 1 (Extruded) Info : Meshing volume 2 (Extruded) Info : Meshing volume 3 (Extruded) Info : Meshing volume 4 (Extruded) Info : Done meshing 3D (0.023414 s) Info : Optimizing mesh... Info : Done optimizing mesh (0.000127 s) Info : 1675 nodes 5184 elements Info : Writing 'mesh/pipe2.msh'... Info : Done writing 'mesh/pipe2.msh' Info : Stopped on Mon Jun 1 23:17:49 2020 /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: v1912 | | \\ / A nd | Website: www.openfoam.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : dd4b8cf30d-20200514 OPENFOAM=1912 patch=200506 Arch : "LSB;label=32;scalar=64" Exec : gmshToFoam -case case mesh/pipe2.msh Date : Jun 01 2020 Time : 23:17:49 Host : houman-Gazelle-Professional PID : 14979 I/O : uncollated Case : /home/houman/projects/upipe/openFoamSample/case nProcs : 1 trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Starting to read mesh format at line 2 Read format version 2.2 ascii 0 Starting to read physical names at line 5 Physical names:9 Surface 2 TunnelOutlet Surface 3 TunnelInlet Surface 4 TunnelWall Surface 5 pipeWalls Surface 6 pipeInlet Surface 7 pipeOutlet Surface 8 wedge0 Surface 9 wedge1 Volume 1 air Starting to read points at line 17 Vertices to be read: 1675 Vertices read:1675 Starting to read cells at line 1695 Cells to be read: 4838 Mapping region 9 to Foam patch 0 Mapping region 7 to Foam patch 1 Mapping region 2 to Foam patch 2 Mapping region 8 to Foam patch 3 Mapping region 3 to Foam patch 4 Mapping region 6 to Foam patch 5 Mapping region 5 to Foam patch 6 Mapping region 4 to Foam patch 7 Mapping region 1 to Foam cellZone 0 Cells: total:1577 hex :0 prism:1510 pyr :35 tet :32 CellZones: Zone Size 0 1577 Patch 0 gets name wedge1 Patch 1 gets name pipeOutlet Patch 2 gets name TunnelOutlet Patch 3 gets name wedge0 Patch 4 gets name TunnelInlet Patch 5 gets name pipeInlet Patch 6 gets name pipeWalls Patch 7 gets name TunnelWall --> FOAM Warning : From function Foam:olyMesh:olyMesh(const Foam::IOobject&, Foam:ointField&&, const cellShapeList&, const faceListList&, const wordList&, const wordList&, const Foam::word&, const Foam::word&, const wordList&, bool) in file meshes/polyMesh/polyMeshFromShapeMesh.C at line 593 Found 3253 undefined faces in mesh; adding to default patch defaultFaces Finding faces of patch 0 Finding faces of patch 1 Finding faces of patch 2 Finding faces of patch 3 Finding faces of patch 4 Finding faces of patch 5 Finding faces of patch 6 Finding faces of patch 7 FaceZones: Zone Size 1 4 5 4 Writing zone 0 to cellZone air and cellSet Writing zone 1 to faceZone pipeOutlet and faceSet Writing zone 5 to faceZone pipeInlet and faceSet End /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: v1912 | | \\ / A nd | Website: www.openfoam.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : dd4b8cf30d-20200514 OPENFOAM=1912 patch=200506 Arch : "LSB;label=32;scalar=64" Exec : checkMesh -case case Date : Jun 01 2020 Time : 23:17:50 Host : houman-Gazelle-Professional PID : 14980 I/O : uncollated Case : /home/houman/projects/upipe/openFoamSample/case nProcs : 1 trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Time = 0 Mesh stats points: 1675 internal points: 0 faces: 5553 internal faces: 2300 cells: 1577 faces per cell: 4.97971 boundary patches: 8 point zones: 0 face zones: 2 cell zones: 1 Overall number of cells of each type: hexahedra: 0 prisms: 1510 wedges: 0 pyramids: 35 tet wedges: 0 tetrahedra: 32 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces... Patch Faces Points Surface topology wedge1 1577 854 ok (non-closed singly connected) pipeOutlet 0 0 ok (empty) TunnelOutlet 17 35 ok (non-closed singly connected) wedge0 1577 854 ok (non-closed singly connected) TunnelInlet 17 35 ok (non-closed singly connected) pipeInlet 0 0 ok (empty) pipeWalls 34 68 ok (non-closed singly connected) TunnelWall 31 64 ok (non-closed singly connected) Checking faceZone topology for multiply connected surfaces... FaceZone Faces Points Surface topology pipeOutlet 4 9 ok (non-closed singly connected) pipeInlet 4 9 ok (non-closed singly connected) Checking basic cellZone addressing... CellZone Cells Points Volume BoundingBox air 1577 1675 0.697106 (0 -2 0) (1.9981 2 0.261052) Checking geometry... Overall domain bounding box (0 -2 0) (1.9981 2 0.261052) Mesh has 3 geometric (non-empty/wedge) directions (1 1 1) Mesh has 3 solution (non-empty) directions (1 1 1) Boundary openness (-1.11534e-17 9.73628e-18 2.85705e-16) OK. Max cell openness = 2.05534e-16 OK. Max aspect ratio = 20.3769 OK. Minimum face area = 2.00566e-05. Maximum face area = 0.0257222. Face area magnitudes OK. Min volume = 7.05952e-07. Max volume = 0.00141272. Total volume = 0.697106. Cell volumes OK. Mesh non-orthogonality Max: 59.066 average: 5.01187 Non-orthogonality check OK. Face pyramids OK. Max skewness = 1.92527 OK. Coupled point location match (average 0) OK. Mesh OK. End Thank you |
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June 3, 2020, 03:12 |
Found the issue
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#2 |
New Member
Join Date: Jan 2019
Posts: 10
Rep Power: 7 |
The issue is that the internal boundary converted from gmsh (using gmshToFoam convertor) is not a patch. It can be converted to a patch using createBaffles.
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July 29, 2020, 15:04 |
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#3 | |
Member
Join Date: Oct 2013
Posts: 92
Rep Power: 12 |
Quote:
I don't any ANY internal boundary patches!! |
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October 26, 2021, 08:27 |
Change the gMsh export settings
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#4 |
New Member
Saikumar Reddy Y
Join Date: May 2020
Posts: 8
Rep Power: 6 |
Just for closing this common issue with gMsh.
One of the most common reasons would be missing the SetFactory("Built-in") command which is the library file for the CAD type approach of geometry generation. The second error would be the export format. Only Version 2 ASCII is compatible with the gmshToFoam command in OpenFOAM. Go to file --> Export --> select .msh in the files --> "DO NOT INCLUDE PARAMETRIC NODES AND ELEMENTS" while exporting. This is also a common source of error. Export the mesh file. Now open the mesh file in notepad/wordpad and check if you $NODES for the nodes, not $ParametricNODES. Also in the $ELEMENTS make sure there is no '0' in the contents. This implies some of the cells have been assigned to patch 0, which needs to be avoided. |
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August 25, 2023, 07:58 |
Similar issue
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#5 |
New Member
Avi
Join Date: Jul 2023
Posts: 2
Rep Power: 0 |
The following is my geo file and I exported it with all elements and no parametric coordinates. I cannot get gmshToFoam to read my physical groups in the boundary file.
Code:
// Gmsh project created on Thu Aug 24 13:42:03 2023 //+ // Backend kernel SetFactory("Built-in"); //+ // Defining the properties of the mesh xoffset = 0; yoffset = 0.5; chlength = 80; chwidth = 4; radius = 1; //+ // Setting mesh characteristic // here, mesh size is the ratio between the perimeter of the cylinder and the number of division on the cylinder (which is 2pi*r/n) meshsize = 0.011; numpts = Round((2*Pi*radius)/meshsize); //+ // Drawing the points Point(1) = {0+xoffset, 0, 0, 1.0}; Point(2) = {0+xoffset, 0+yoffset, 0, 1.0}; Point(3) = {xoffset, radius+yoffset, 0, 1.0}; Point(4) = {xoffset, -radius+yoffset, 0, 1.0}; Point(5) = {radius+xoffset, yoffset, 0, 1.0}; Point(6) = {-radius+xoffset, yoffset, 0, 1.0}; Point(7) = {-0.25*chlength, 0.5*chwidth,0,1.0}; Point(8) = {-0.25*chlength, 0, 0, 1.0}; Point(9) = {-0.25*chlength, -0.5*chwidth, 0, 1.0}; Point(10) = {0.75*chlength, 0.5*chwidth, 0, 1.0}; Point(11) = {0.75*chlength, 0, 0, 1.0}; Point(12) = {0.75*chlength, -0.5*chwidth, 0, 1.0}; Point(13) = {0.5*chwidth+xoffset, 0.5*chwidth, 0, 1.0}; Point(14) = {-0.5*chwidth+xoffset, 0.5*chwidth, 0, 1.0}; Point(15) = {-0.5*chwidth+xoffset, -0.5*chwidth, 0, 1.0}; Point(16) = {0.5*chwidth+xoffset, -0.5*chwidth, 0, 1.0}; Point(17) = {0.5*chwidth+xoffset, 0, 0, 1.0}; Point(18) = {-0.5*chwidth+xoffset, 0, 0, 1.0}; Point(19) = {0+xoffset, 0.5*chwidth, 0, 1.0}; Point(20) = {0+xoffset, -0.5*chwidth, 0, 1.0}; //+ // Drawing the walls and other lines Line(1) = {7, 14}; Line(2) = {14, 19}; Line(3) = {19, 13}; Line(4) = {13, 10}; Line(5) = {10, 11}; Line(6) = {11, 12}; Line(7) = {12, 16}; Line(8) = {16, 20}; Line(9) = {20, 15}; Line(10) = {15, 9}; Line(11) = {9, 8}; Line(12) = {8, 7}; Line(13) = {14, 18}; Line(14) = {18, 15}; Line(15) = {13, 17}; Line(16) = {17, 16}; Line(17) = {18,8}; Line(18) = {17,11}; //+ // Drawing the cylinder Point(21) = {radius*Cos(Pi/4)+xoffset,radius*Sin(Pi/4)+yoffset, 0, 1.0}; Point(22) = {-radius*Cos(Pi/4)+xoffset,radius*Sin(Pi/4)+yoffset, 0, 1.0}; Point(23) = {-radius*Cos(Pi/4)+xoffset,-radius*Sin(Pi/4)+yoffset, 0, 1.0}; Point(24) = {radius*Cos(Pi/4)+xoffset,-radius*Sin(Pi/4)+yoffset, 0, 1.0}; Circle(19) = {3, 2, 22}; Circle(20) = {22, 2, 6}; Circle(21) = {6, 2, 23}; Circle(22) = {23, 2, 4}; Circle(23) = {4, 2, 24}; Circle(24) = {24, 2, 5}; Circle(25) = {5, 2, 21}; Circle(26) = {21, 2, 3}; Line(27) = {19, 3}; Line(28) = {14, 22}; Line(29) = {18, 6}; Line(30) = {15, 23}; Line(31) = {20, 4}; Line(32) = {16, 24}; Line(33) = {17, 5}; Line(34) = {13, 21}; //+ // Setting mesh size through transfinite curves Transfinite Curve {12, 11, 13, 14, 2, 3, 9, 8, 15, 16, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26} = Round(numpts/8) Using Progression 1; Transfinite Curve {-1, 17, 10} = 22 Using Progression 1.2; Transfinite Curve {4, 18, -7} = 29 Using Progression 1.2; Transfinite Curve {-30, -31, -32, -33, -34, -27, -28, -29} = Round(numpts/8) Using Progression 1.05; //+ // Drawing surfaces Curve Loop(1) = {1, 13, 17, 12}; Plane Surface(1) = {1}; Curve Loop(2) = {10, 11, -17, 14}; Plane Surface(2) = {2}; Curve Loop(3) = {13, 29, -20, -28}; Plane Surface(3) = {3}; Curve Loop(4) = {14, 30, -21, -29}; Plane Surface(4) = {4}; Curve Loop(5) = {2, 27, 19, -28}; Plane Surface(5) = {5}; Curve Loop(6) = {22, -31, 9, 30}; Plane Surface(6) = {6}; Curve Loop(7) = {3, 34, 26, -27}; Plane Surface(7) = {7}; Curve Loop(8) = {23, -32, 8, 31}; Plane Surface(8) = {8}; Curve Loop(9) = {34, -25, -33, -15}; Plane Surface(9) = {9}; Curve Loop(10) = {33, -24, -32, -16}; Plane Surface(10) = {10}; Curve Loop(11) = {4, 5, -18, -15}; Plane Surface(11) = {11}; Curve Loop(12) = {7, -16, 18, 6}; Plane Surface(12) = {12}; // Making transfinite surfaces Transfinite Surface {1} = {7, 8, 18, 14}; Transfinite Surface {2} = {8, 9, 15, 18}; Transfinite Surface {3} = {14, 18, 6, 22}; Transfinite Surface {4} = {18, 15, 23, 6}; Transfinite Surface {5} = {14, 22, 3, 19}; Transfinite Surface {6} = {23, 15, 20, 4}; Transfinite Surface {7} = {19, 3, 21, 13}; Transfinite Surface {8} = {4, 20, 16, 24}; Transfinite Surface {9} = {21, 5, 17, 13}; Transfinite Surface {10} = {5, 24, 16, 17}; Transfinite Surface {11} = {13, 17, 11, 10}; Transfinite Surface {12} = {17, 16, 12, 11}; //+ // Recombine Surfaces Recombine Surface {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}; //+ // Extrude to create volume Extrude {0, 0, 1} { Surface{1}; Surface{2}; Surface{3}; Surface{4}; Surface{5}; Surface{6}; Surface{7}; Surface{8}; Surface{9}; Surface{10}; Surface{11}; Surface{12}; Layers {1}; Recombine; } //+ // Adding Physical Groups Physical Surface("inlet", 299) = {55, 69}; Physical Surface("beforeCylinder", 300) = {47, 77}; Physical Surface("afterCylinder", 301) = {231, 253}; Physical Surface("aboveCylinder", 302) = {135}; Physical Surface("belowCylinder", 303) = {157}; Physical Surface("outlet", 304) = {267, 297}; Physical Surface("walls", 305) = {43, 131, 175, 263, 65, 161, 205, 285}; Physical Surface("cylinder", 306) = {139, 183, 223, 245, 197, 153, 117, 95}; Physical Surface("frontAndBack", 307) = {56, 1, 78, 2, 276, 11, 298, 12, 100, 3, 122, 4, 144, 5, 188, 7, 232, 9, 10, 254, 210, 8, 166, 6}; 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gmshtofoam patch, gmshtofoam problem |
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